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what's difference between a read marked by "sam FLAG 1024" and marked by " PG:markduplicates" ?
1 . when I run the following command : "samtools view -h -f 1024 bwa.raw.bam " , then can not get any reads , so I think BWA do not markduplicates to use" FLAG 1024". 2 after I deal with bwa.raw.bam with using picard-markduplicates , "samtools view -h -f 1024 baw.raw.markdup.bam " , I got some reads with the below marks : FLAG : 1187 PG:Z:MarkDuplicates SO i got a question : I know the option "-f 1024" is just for optical or pcr dups , but I do not know which software modify "FLAG" to add "1024" ?? according to 1 , I think BWA do not do that becasue no reads found . however ,according to 2 , I got reads markd by "FLAG 1024", so I guess when I do the picard-markduplicates step , picard will modify sam flag ?? ,not just add "PG:Z:MarkDuplicates" .